Hi all I've seen this asked before in relation to limma but I couldn't find an answer so... I'm getting this warning 8 times in the R console when I quit out of affylmGUI after computing contrasts and exporting toptables In ebayes(fit = fit, proportion = proportion, stdev.coef.lim = stdev.coef.lim) : Estimation of var.prior failed - set to default value Anyone have any idea what it means?. Thanks Glyn Bradley (postdoc at mycib.ac.uk) -- Dr Glyn Bradley Postdoctoral Research Fellow - Bioinformatics and Systems Modelling Multidisciplinary Centre for Integrative Biology (MyCIB) University of Nottingham UK This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.